-->
Receptor
PDB id Resolution Class Description Source Keywords
4D56 2.1 Å NON-ENZYME: OTHER UNDERSTANDING BI-SPECIFICITY OF A-DOMAINS PLANKTOTHRIX AGARDHII HYDROLASE NON-RIBOSOMAL PEPTIDE SYNTHETASE ADENYLATION A
Ref.: STRUCTURAL ELUCIDATION OF THE BISPECIFICITY OF A DO A BASIS FOR ACTIVATING NON-NATURAL AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 8833 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1494;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
TYR AMP A:1491;
Valid;
none;
submit data
510.4 n/a P(=O)...
PO4 A:1493;
A:1492;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4D57 2 Å NON-ENZYME: OTHER UNDERSTANDING BI-SPECIFICITY OF A-DOMAINS PLANKTOTHRIX AGARDHII TRANSCRIPTION NON-RIBOSOMAL PEPTIDE SYNTHETASE ADENYLATIONDOMAIN
Ref.: STRUCTURAL ELUCIDATION OF THE BISPECIFICITY OF A DO A BASIS FOR ACTIVATING NON-NATURAL AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 8833 2015
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
5 1AMU - AMP C10 H14 N5 O7 P c1nc(c2c(n....
6 5N81 - 8Q2 C22 H25 N7 O8 S C#CCOc1ccc....
7 5N82 - 8PZ C19 H23 N7 O7 S c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TYR AMP; Similar ligands found: 259
No: Ligand ECFP6 Tc MDL keys Tc
1 TYR AMP 1 1
2 DAL AMP 0.736842 0.933333
3 ARG AMP 0.695238 0.878049
4 GAP 0.684211 0.921053
5 YAP 0.657143 0.973333
6 MYR AMP 0.622642 0.843373
7 4AD 0.605769 0.947368
8 ADP PO3 0.59596 0.918919
9 ADP VO4 0.582524 0.883117
10 VO4 ADP 0.582524 0.883117
11 CA0 0.581633 0.896104
12 A 0.580645 0.868421
13 AMP 0.580645 0.868421
14 A2D 0.578947 0.894737
15 5AL 0.578431 0.907895
16 ADP ALF 0.572816 0.85
17 ALF ADP 0.572816 0.85
18 FA5 0.567568 0.96
19 SRP 0.567308 0.934211
20 BA3 0.56701 0.894737
21 A12 0.56701 0.860759
22 AP2 0.56701 0.860759
23 YSA 0.5625 0.825581
24 ABM 0.5625 0.846154
25 B4P 0.561224 0.894737
26 AP5 0.561224 0.894737
27 ADP 0.561224 0.87013
28 LPA AMP 0.560345 0.843373
29 8QN 0.551402 0.907895
30 ADP BMA 0.550459 0.921053
31 PAJ 0.546296 0.841463
32 AMO 0.546296 0.934211
33 B5V 0.545455 0.934211
34 WAQ 0.545455 0.886076
35 A A 0.545455 0.894737
36 HEJ 0.544554 0.87013
37 ATP 0.544554 0.87013
38 50T 0.544554 0.835443
39 AMP DBH 0.54386 0.921053
40 SRA 0.541667 0.825
41 DLL 0.541284 0.933333
42 1ZZ 0.540541 0.821429
43 PTJ 0.540541 0.851852
44 AT4 0.54 0.8375
45 SON 0.54 0.909091
46 AN2 0.54 0.858974
47 AR6 0.539216 0.894737
48 APC 0.539216 0.860759
49 APR 0.539216 0.894737
50 PRX 0.539216 0.825
51 AQP 0.539216 0.87013
52 5FA 0.539216 0.87013
53 9ZA 0.537037 0.8625
54 OOB 0.537037 0.933333
55 9ZD 0.537037 0.8625
56 3UK 0.536364 0.921053
57 AU1 0.534653 0.848101
58 M33 0.534653 0.858974
59 ADX 0.534653 0.788235
60 AD9 0.533981 0.848101
61 ADV 0.533981 0.884615
62 AGS 0.533981 0.82716
63 RBY 0.533981 0.884615
64 SAP 0.533981 0.82716
65 AMP NAD 0.532258 0.959459
66 LAD 0.531532 0.8875
67 9SN 0.530973 0.875
68 ACP 0.529412 0.871795
69 00A 0.527273 0.886076
70 NB8 0.526786 0.898734
71 ME8 0.526786 0.865854
72 FYA 0.526786 0.907895
73 ATP A A A 0.526316 0.932432
74 AHZ 0.525424 0.843373
75 AF3 ADP 3PG 0.525 0.8875
76 A22 0.513761 0.883117
77 MAP 0.513761 0.82716
78 AHX 0.513514 0.875
79 TXA 0.513274 0.884615
80 B5Y 0.513043 0.922078
81 B5M 0.513043 0.922078
82 ACQ 0.509434 0.871795
83 T99 0.509434 0.8375
84 ANP 0.509434 0.848101
85 TAT 0.509434 0.8375
86 5SV 0.509091 0.785714
87 9X8 0.508929 0.85
88 OAD 0.508929 0.896104
89 NAJ PZO 0.507812 0.875
90 ADQ 0.504505 0.896104
91 A1R 0.504505 0.8625
92 PR8 0.504425 0.876543
93 NAI 0.504132 0.8625
94 TYM 0.5 0.96
95 LMS 0.5 0.767442
96 3OD 0.5 0.896104
97 ATF 0.5 0.8375
98 NAD 0.496063 0.933333
99 YLB 0.495935 0.845238
100 YLP 0.495868 0.845238
101 7MD 0.495798 0.865854
102 AR6 AR6 0.495798 0.945946
103 25A 0.495495 0.894737
104 6YZ 0.495413 0.871795
105 NAJ PYZ 0.492424 0.833333
106 NAQ 0.492424 0.875
107 NSS 0.491071 0.804598
108 A3R 0.491071 0.8625
109 AOC 0.49 0.779221
110 ZID 0.488722 0.921053
111 A3D 0.488372 0.921053
112 80F 0.488372 0.86747
113 LAQ 0.487603 0.821429
114 NVA LMS 0.486726 0.777778
115 D3Y 0.486486 0.842105
116 G5A 0.485981 0.784091
117 5AS 0.485437 0.725275
118 7MC 0.483871 0.845238
119 5CD 0.483871 0.763158
120 AP0 0.483871 0.829268
121 4UU 0.483333 0.897436
122 GA7 0.483333 0.860759
123 XAH 0.483051 0.843373
124 25L 0.482759 0.883117
125 LEU LMS 0.482456 0.777778
126 DND 0.479675 0.934211
127 NXX 0.479675 0.934211
128 DQV 0.479339 0.907895
129 4UV 0.478992 0.897436
130 OMR 0.475806 0.811765
131 TXE 0.475806 0.8625
132 JB6 0.474138 0.8625
133 BIS 0.474138 0.817073
134 NAE 0.473684 0.897436
135 TSB 0.473214 0.761364
136 A5A 0.472727 0.770115
137 YLC 0.472 0.865854
138 48N 0.471545 0.875
139 AFH 0.471074 0.864198
140 AYB 0.46875 0.835294
141 SSA 0.468468 0.784091
142 NAX 0.467742 0.876543
143 TXD 0.467742 0.8625
144 ADN 0.467391 0.776316
145 XYA 0.467391 0.776316
146 RAB 0.467391 0.776316
147 TAD 0.467213 0.841463
148 IOT 0.464567 0.835294
149 54H 0.464286 0.752809
150 52H 0.464286 0.744444
151 VMS 0.464286 0.752809
152 U A 0.462121 0.886076
153 4TA 0.461538 0.878049
154 9K8 0.461538 0.73913
155 COD 0.461538 0.795455
156 G A A A 0.461538 0.875
157 YLA 0.460938 0.845238
158 5CA 0.460177 0.784091
159 53H 0.460177 0.744444
160 EAD 0.459854 0.853659
161 5X8 0.457944 0.815789
162 5N5 0.457447 0.753247
163 P1H 0.457143 0.833333
164 NDE 0.457143 0.909091
165 GEK 0.45614 0.810127
166 4UW 0.456 0.864198
167 6V0 0.456 0.851852
168 GTA 0.455285 0.843373
169 M24 0.455224 0.853659
170 F2R 0.453846 0.845238
171 P5A 0.452991 0.75
172 GSU 0.452991 0.804598
173 A4D 0.452632 0.753247
174 DSZ 0.452174 0.804598
175 LSS 0.452174 0.766667
176 G3A 0.45082 0.851852
177 NDC 0.450704 0.875
178 A G 0.450382 0.886076
179 NMN AMP PO4 0.450382 0.897436
180 3DH 0.45 0.734177
181 139 0.449612 0.853659
182 DTA 0.44898 0.769231
183 M2T 0.44898 0.719512
184 A3P 0.447619 0.868421
185 8X1 0.447368 0.758242
186 G5P 0.447154 0.851852
187 DZD 0.44697 0.864198
188 BT5 0.44697 0.835294
189 U A G G 0.44697 0.886076
190 CNA 0.446154 0.934211
191 N0B 0.445255 0.86747
192 UP5 0.444444 0.873418
193 SFG 0.444444 0.802632
194 PO4 PO4 A A A A PO4 0.444444 0.905405
195 YLY 0.444444 0.835294
196 SMM 0.442478 0.752941
197 Z5A 0.442029 0.825581
198 SAM 0.441441 0.759036
199 KAA 0.440678 0.758242
200 EP4 0.438776 0.716049
201 T5A 0.438462 0.845238
202 8PZ 0.438017 0.804598
203 6RE 0.436893 0.765432
204 PAP 0.436364 0.857143
205 A U 0.434109 0.897436
206 A4P 0.434109 0.804598
207 A2P 0.433962 0.855263
208 A A A 0.432203 0.907895
209 4YB 0.432 0.806818
210 3AM 0.431373 0.831169
211 MTA 0.43 0.734177
212 S7M 0.429825 0.759036
213 WSA 0.429688 0.813953
214 N01 0.42963 0.933333
215 J7C 0.428571 0.753086
216 ADJ 0.427481 0.833333
217 UPA 0.426357 0.8625
218 4TC 0.426357 0.875
219 7D5 0.425743 0.7875
220 EEM 0.424779 0.759036
221 S4M 0.424528 0.693182
222 ATR 0.423423 0.844156
223 SA8 0.423423 0.756098
224 KB1 0.421488 0.768293
225 NJP 0.421053 0.922078
226 SAI 0.419643 0.78481
227 SAH 0.419643 0.794872
228 A C A C 0.419118 0.875
229 NEC 0.419048 0.708861
230 0WD 0.41791 0.851852
231 3NZ 0.416667 0.833333
232 7C5 0.416 0.822785
233 8Q2 0.415385 0.797753
234 0UM 0.415254 0.746988
235 A3N 0.415094 0.725
236 IMO 0.415094 0.855263
237 2A5 0.414414 0.825
238 A2R 0.413793 0.883117
239 ZAS 0.413462 0.772152
240 PPS 0.412281 0.767442
241 7D3 0.411215 0.790123
242 GJV 0.411215 0.756098
243 A5D 0.410714 0.769231
244 7D4 0.409091 0.790123
245 ITT 0.409091 0.844156
246 U A C C 0.408759 0.886076
247 2AM 0.407767 0.820513
248 649 0.407692 0.788889
249 MAO 0.407407 0.744186
250 BTX 0.407407 0.823529
251 4CA 0.406667 0.8
252 DSH 0.40566 0.731707
253 A3G 0.40566 0.805195
254 NAP 0.404255 0.921053
255 V3L 0.403509 0.894737
256 6AD 0.4 0.797619
257 A7D 0.4 0.759494
258 A3S 0.4 0.815789
259 5AD 0.4 0.706667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4D57; Ligand: ARG AMP; Similar sites found with APoc: 145
This union binding pocket(no: 1) in the query (biounit: 4d57.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 5CQG 55C 1.22164
3 3EXS 5RP 1.35747
4 2G7C GLA GAL NAG 1.96078
5 1Q19 SSC 1.98807
6 1H5R THM 2.04778
7 2GJP MAL 2.06186
8 1H3F TYE 2.08333
9 3B2Q AES 2.1322
10 3LTW HLZ 2.14286
11 2AAZ CB3 2.2082
12 3TAO PGH 2.24719
13 1BW9 PPY 2.24719
14 1BXG HCI 2.24719
15 1C1X HFA 2.25352
16 2A9W GA9 2.27273
17 5C9P FUC 2.3622
18 1H74 ILE 2.36486
19 1L7P SEP 2.36967
20 1L7N ALF 2.36967
21 4B2D SER 2.37226
22 1V6A TRE 2.40964
23 5O2N FLC 2.44328
24 3KCC CMP 2.44328
25 5VKM GAL SIA 2.46914
26 2Y4O DLL 2.48307
27 5WXU FLC 2.50522
28 2ZUX RAM 2.53807
29 1D8T GDP 2.54453
30 1C3X 8IG 2.63158
31 1J1R ADE 2.68199
32 6E1Q CFA 2.79232
33 3GVL SLB SIA 2.79232
34 3QPB R1P 2.83688
35 1W8S FBP 3.04183
36 5LX6 78P 3.14136
37 5H4S RAM 3.16901
38 3A06 NDP 3.19149
39 3ZZH NLG 3.25733
40 3ZZH ARG 3.25733
41 5W5R PYR 3.34928
42 5FPE 3TR 3.35917
43 3UEC ALA ARG TPO LYS 3.42466
44 5KOD AMP 3.4904
45 4PTN GXV 3.4904
46 3BJE R1P 3.72493
47 5XNC MTA 3.77358
48 3JQQ A2P 3.79747
49 2BQP GLC 3.84615
50 4KBA 1QM 3.92749
51 4BG4 ARG 3.93258
52 1X8X TYR 4.03727
53 2YPI PGA 4.04858
54 1S8G DAO 4.13223
55 1Q6O LG6 4.16667
56 5M6N 7H9 4.23729
57 4OEV OXL 4.25101
58 4URX HXY 4.31212
59 5BN3 ADP 4.363
60 1GPM AMP 4.38095
61 5DEQ ARA 4.38596
62 1E5F PLP 4.45545
63 5MB4 NAG 4.48878
64 5IGL BMF 4.51613
65 3A6T 8OG 4.65116
66 1FDJ 13P 4.6832
67 1QDS PGA 4.78088
68 4V3C C 4.89691
69 2IV3 UDP 4.97076
70 4TS1 TYR 5.01567
71 2F6U CIT 5.12821
72 1BC5 ACE ASN TRP GLU THR PHE 5.20446
73 2WPW ACO 5.60472
74 3FSY SCA 5.72289
75 1LYX PGA 5.75916
76 4EPM AMP 5.85198
77 1C3M MAN MAN 6.12245
78 2PKA BEN 6.25
79 1QD0 RR6 6.25
80 1VKF CIT 6.38298
81 5XQW 8EU 6.45161
82 3ZGJ RMN 6.469
83 6BSW UDP 6.50888
84 6G5J EM8 6.66667
85 2X1L ADN 6.87023
86 3W6X HZP 6.9869
87 1L5Y BEF 7.09677
88 4OVZ P85 7.27848
89 4OFJ HIS 7.39958
90 4Z87 GDP 7.80952
91 5TCI MLI 7.97101
92 3MYZ TFX 8
93 1QAW TRP 8.10811
94 3P2H NOO 8.45771
95 3KIF GDL 8.49057
96 1HSL HIS 8.82353
97 2BVE PH5 9.2437
98 1I1E DM2 9.77312
99 3T64 DU3 9.94475
100 2WG9 OCA 10.7692
101 4NAE 1GP 11.1111
102 2VQZ MGT 12.0482
103 1YZG GDP 12.2905
104 3H0L ADP 17.0213
105 3HCH RSM 17.1233
106 1SW0 PGA 18.1452
107 4JEJ 1GP 22.9508
108 3CT5 NAG NAG NAG 23.2704
109 5MST AMP 25.4799
110 5MST FUM 25.4799
111 5MSD BEZ 28.0977
112 5MSD AMP 28.0977
113 5HM3 649 28.4468
114 5EY9 5SV 28.9703
115 3KXW 1ZZ 32.1117
116 5D6J ATP 32.2862
117 1LES GLC FRU 32.6923
118 5OE4 3UK 36.3636
119 1PG4 PRX 37.1728
120 1PG4 COA 37.1728
121 1RY2 AMP 37.3473
122 3IES M24 38.657
123 1MDB AMP DBH 39.5176
124 2D1S SLU 39.5985
125 3C5E ATP 40.1754
126 4FUT ATP 40.7555
127 5WM2 SAL 41.1348
128 5WM2 AMP 41.1348
129 1V25 ANP 41.22
130 5BSR COA 41.6974
131 5BSR AMP 41.6974
132 4GXQ ATP 41.6996
133 4RLQ 3SK 42.0039
134 4DG8 AMP 42.0593
135 3O84 HTJ 42.4632
136 5X8G S0N 43.0928
137 2V7B BEZ 43.4783
138 3NYQ AMP 43.5644
139 3NYQ MCA 43.5644
140 3CW9 AMP 43.8492
141 3CW9 01A 43.8492
142 4OXI GAP 44.2708
143 5IE3 OXD 44.358
144 5IE3 AMP 44.358
145 5C5H 4YB 45.4746
APoc FAQ
Feedback